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Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage difference between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.

Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet, it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence and introgression on plumage differentiation between ecologically similar allopatric replacements of Andean cloud forest birds. Through analyses of short-read genome-wide sequences from over 160 individuals in 16 codistributed lineages, I found that plumage divergence is associated with deep genetic divergence, implicating a prominent role of geographic isolation in speciation. By contrast, lineages that lack plumage divergence across the same geographic barrier are more recently isolated or exhibit a signature of secondary genetic introgression, indicating a negative relationship between gene flow and divergence in phenotypic traits important to speciation. My results suggest that the evolutionary outcomes of cycles of isolation and divergence in this important theatre of biotic diversification are sensitive to time spent in the absence of gene flow.

Males of sexually dimorphic species often appear more divergent among taxa than do females, so it is often assumed that evolutionary changes have occurred primarily in males. Yet, sexual dimorphisms can result from historical changes in either or both of the sexes, and few previous studies have investigated such patterns using phylogenetic methods. Here, we describe the evolution of male and female plumage colors in the grackles and allies (Icteridae), a songbird clade with a broad range in levels of sexual dichromatism. Using a model of avian perceptual color space, we calculated color distances within and among taxa on a molecular phylogeny. Our results show that female plumage colors have changed more dramatically than male colors in the evolutionary past, yet male colors are significantly more divergent among species today. Historical increases in dichromatism have involved changes in both sexes, whereas decreases in dichromatism have nearly always involved females evolving rapidly to look like males. Dichromatism is also associated with mating system in this group, with monogamous taxa tending to exhibit relatively low levels of sexual dichromatism. Our findings suggest that, despite appearances, female plumage evolution plays a more prominent role in sexual dichromatism than is generally assumed.

Historical scenarios of evolution of avian plumage coloration have been called into question with the discoveries that most birds can see UV light (which normal humans cannot), and that UV-reflecting plumages are widespread in birds. Several examples of sexual dichromatism not detectable with human visual capabilities suggest that our categorizations of plumages as sexually mono- or dichromatic might often be incorrect. Nonetheless, given the limited taxonomic scope of those examples, the vast majority of sexually monochromatic birds are still treated as such without question in avian research. Herein, I show that >90% of 139 species, in a broad sampling of presumed sexually monochromatic passerine birds, were actually sexually dichromatic from an avian visual perspective, based on comparisons of plumage reflectance data using a visual model of color discrimination thresholds. The taxonomic ubiquity of this result suggests that many existing interpretations of evolutionary patterns of sexual dichromatism in birds are erroneous. The visual model used herein provides a method for quantifying sexual dichromatism, revealing that most (58.7%) feather patches sampled lie along a continuum of dichromatism between avian and human discriminatory abilities and could represent unrecognized sexually selected signals. Sexual dichromatism in this study rarely resulted from intersexual differences in UV coloration alone, emphasizing the need for analysis of bird coloration in relation to the full extent of avian visual discriminatory abilities, including, but not limited to, UV-visual capabilities.

Sexual dichromatism in birds is often attributed to selection for elaboration in males. However, evolutionary changes in either sex can result in plumage differences between them, and such changes can result in either gains or losses of dimorphism. We reconstructed the evolution of plumage colors in both males and females of species in Maluridae, a family comprising the fairy‐wrens (Malurus, Clytomias, Sipodotus), emu‐wrens (Stipiturus), and grasswrens (Amytornis). Our results show that, across species, males and females differ in their patterns of color evolution. Male plumage has diverged at relatively steady rates, whereas female coloration has changed dramatically in some lineages and little in others. Accordingly, in comparisons against evolutionary models, plumage changes in males best fit a Brownian motion (BM) model, whereas plumage changes in females fit an Ornstein Uhlenbeck (OU) multioptimum model, with different adaptive peaks corresponding to distributions in either Australia or New Guinea. Levels of dichromatism were significantly associated with latitude, with greater dichromatism in more southerly taxa. Our results suggest that current patterns of plumage diversity in fairy‐wrens are a product of evolutionary changes in both sexes, driven in part by environmental differences across the distribution of the family. Illustration of both males and females of five species representative of the Maluridae family showing the range of plumage dimorphism present in the family: (A) Wallace's fairy‐wren (Sipodotus wallacii), (B) Southern emu‐wren (Stipiturus malachurus), (C) splendid fairy‐wren (Malurus splendens), (D) lovely fairy‐wren (Malurus amabilis), and (E) white‐shouldered fairy‐wren (Malurus alboscapulatus). Males are illustrated above females in each species pair.

Avian color patterns function in varied behavioral contexts, most being produced by only a handful of mechanisms including feather nanostructures and pigments. Within a clade, colors may not occupy the entire available space, and incorporating complementary colors may increase the contrast and efficacy of visual signals. Here, we describe plumage patterns in four ecologically and phylogenetically diverse bird families to test whether they possess complementary colors. We present evidence that plumage colors in each clade cluster along a line in tetrachromatic color space. Additionally, we present evidence that in three of these clades, this line contains colors on opposite sides of a line passing through the achromatic point (putatively complementary colors, presenting higher chromatic contrast). Finally, interspecific color variation over at least some regions of the body is not constrained by phylogenetic relatedness. By describing plumage patterns in four diverse lineages, we add to the growing body of literature suggesting that the diversity of bird visual signals is constrained. Further, we tentatively hypothesize that in at least some clades possessing bright colors, species-specific plumage patterns may evolve by swapping the distributions of a complementary color pair. Further research on other bird clades may help confirm whether these patterns are general across bird families.

Local adaptation is often implicated as a driver of speciation and diversity, but measuring local variation within a species can be difficult. Many taxa endemic to salt marshes exhibit a phenotypic trait called salt marsh melanism, in which salt marsh endemics have a darker or grayer integument than their freshwater congeners. The repeated occurrence of salt marsh melanism across distantly related taxa in similar environments suggests a role for local selection in maintaining this trait. We quantitatively explored variation in plumage characteristics for four subspecies of the Song Sparrow (Melospiza melodia) in the San Francisco Bay area. These subspecies are restricted to habitats of varying salinity and climate, and are considered a classic example of ecologically based variation on a local scale. To analyze plumage color, we employed a digital photographic technique which was quantitative, able to deal with pattern variation, and independent of a particular visual system. Although no single plumage measure distinguished among all four subspecies, combining the measures allowed reliable assignment of most specimens. Using a discriminant analysis with five measures of plumage color, we were able to classify 75% of specimens to the correct subspecies, well above the 25% correct classification expected due to chance. The three subspecies inhabiting more saline environments (M. m. pusillula, M. m. samuelis, and M. m. maxillaris) were either darker (lower luminance) or grayer (lower red dominance) than the inland subspecies M. m. gouldii, supporting the pattern of salt marsh melanism observed in other taxa.

The importance of the formation of the Panamanian land bridge for mammalian diversification in the New World is well documented; however, studies investigating the role of this land bridge in avian diversification have only recently been reported. We used mitochondrial DNA data to reconstruct the phylogeny of a group of lowland tanagers (Thraupidae) that contains species distributed in both Central America and South America. Phylogenetic analyses identified a clade that includes all 26 species in the genera Tachyphonus, Ramphocelus, Eucometis, Lanio, Trichothraupis, Coryphospingus, and Rhodospingus. Three of these species (Rhodospingus cruentus, Coryphospingus cucullatus, and C. pileatus) have traditionally been classified with the finches (Emberizidae); here, we show that they are tanagers. The genus Tachyphonus is polyphyletic, with some species more closely related to species in the genus Ramphocelus than they are to other Tachyphonus. The ancestor of the entire clade was distributed in South America or was widespread there and in Central America. Reconstructing the biogeographic history of this group showed a dispersal bias from South America to Central America. Nine dispersal events were inferred, and eight of these involve dispersals from South America to Central America. Temporally, most dispersal events coincide with or postdate the final formation of the Panamanian isthmus. We also used our phylogeny to investigate plumage evolution. Two species are sexually monochromatic, and this condition was derived from sexual dichromatism through the evolution of more colorful female plumage. Although 11 species in the clade have crests, this feature evolved no more than twice within the group.

We present the first molecular phylogenetic hypothesis for Knipolegus (black-tyrants), a widespread genus of South American tyrant-flycatchers, based on nuclear and mitochondrial DNA sequences. Bayesian and maximum-likelihood analyses support three clades within Knipolegus, one confined to northern South America, one confined to southeast Brazil, and one confined to the Southern Cone and southern Andes. Within each clade, two or more species are broadly sympatric or parapatric, overlapping in general distribution but differing in habitat specialization. Maximum-likelihood ancestral state reconstructions using an equal-rate stochastic model support a single origin of austral migration in the southern group. Contrasting with these strong geographic patterns, ancestral state reconstructions of plumage and display evolution were more complex, with multiple inferred character-state changes. Ancestral state reconstructions suggest a sexually dimorphic ancestor of Knipolegus, and sexually similar plumages are the result of three independent character-state changes: one in male plumage and two in female plumage. Ancestral state reconstructions support the conclusion that flight displays with mechanical sounds originated in the Knipolegus ancestor, and loss of mechanical sounds in flight displays occurred twice.

A recent phylogenetic survey of the New World orioles (genus Icterus; Omland et al. 1999) suggested that the Baltimore Oriole (I. galbula) and the Black-backed Oriole (I. abeillei) are sister taxa. That survey examined mitochondrial DNA (mtDNA) from a single representative of each species in the genus. Here, we examine mtDNA sequences from 15 Black-backed and 20 Baltimore Orioles. The two species appear to be very recently diverged, with average sequence divergences for both cytochrome b (cyt b) and the control region indicating a probable late Pleistocene split. Despite this very recent divergence, there is one fixed base-pair difference between the species in cyt b and another in the control region, suggesting that one or both species have undergone a bottleneck during or since speciation. This molecular evidence of recent divergence suggests that male plumage differences between Black-backed and Baltimore Orioles evolved very rapidly. Especiación Reciente entre Icterus galbula y Icterus abeillei Resumen. Un estudio filogenético reciente de los orioles del Nuevo Mundo (género Icterus; Omland, et al. 1999) sugiere que Icterus galbula e I. abeillei son taxa hermanos. En aquel estudio se examinó el ADN mitocondrial de un sólo representante de cada especie del género. En este estudio examinamos secuencias de ADN mitocondrial de 15 individuos de I. abeillei y 20 de I. galbula. Las dos especies parecen haber divergido recientemente con una separación promedio de las secuencias nucleotídicas en citocromo b y la región de control que indica que la divergencia ocurrió probablemente a fines del Pleistoceno. A pesar de haber divergido tan recientemente, existe una diferencia fija de un par de bases en la secuencia nucleotídica entre las dos especies en citocromo b y otra diferencia fija en la secuencia nucleotídica de la región de control, lo cual sugiere que una o ambas especies han sufrido un efecto de cuello de botella desde o durante el proceso de especiación. Esta evidencia molecular de divergencia reciente sugiere que los elementos del plumaje en los machos evolucionaron muy rápidamente entre I. abeillei e I. galbula.